I’m thrilled that my writing has been selected for inclusion in The Best Australian Science Writing 2015! The anthology is edited by Bianca Nogrady and published by NewSouth Books, and was launched this week. I can’t wait to hold my copy in my hot little hands. The fact that I’m not currently holding it is entirely my own fault for moving house and forgetting to tell NewSouth Books where to send my copy, as if they were supposed to just sense my location somehow. So I must wait a little longer for mail-forwarding to do its thing. I’m not finding the wait easy, not simply because of the tangibility, that buzz of physically holding a published story, but also because the whole thing promises to be a great read — I mean just look at that list of contributors. I’ve found myself in some wonderful company here.

The Best Australian Science Writing 2015 is available now from NewSouth Books and will soon be available internationally on Amazon. Happy reading!

Well, this has certainly turned out to be a hectic year. I can’t complain, though, it’s been chaotic in a good way. Indeed, there have been some brilliant adventures. At one point, I even climbed a mountain quite by accident. Some of my friends might point out that this is becoming an unfortunate habit of mine and that I should really start making a point of consulting topology maps before ever leaving the house. They are of course right, but more on that later.

For now, I’m glad that it’s all calming down now and I can settle back into a writing routine, so watch this space for more science and life. Ideas are brewing.

In the mean time, say hello to this little guy, who we met in the wilds of Tasmania.

Humans have been marvelling at these tiny creatures for eons, baffled by their fascinating ability to hover and their stunning wing speed. For quite some time, it was thought that hummingbirds had flight dynamics closer to that of insects. Even with decades of analysis with high speed cameras, it was only relatively recently that high-tech analysis began to reveal how hummingbirds accomplish their unique aerodynamic trick.

Hummingbirds weigh between 2 and 20 grams, most less than 5 grams. And this poses another interesting problem: how do hummingbirds contend so well with rain and strong winds? It’s a question that points to a significant gap in our knowledge about flying animals in general: we just don’t know that much about the mechanisms they use to handle complex changes in air flow.

The advertisements were enticing. They turned up regularly across England for decades. Posters. Newspaper ads. Leaflets. They offered time away in the countryside near Salisbury. Fresh air. Relaxation. Free meals. Not only that, you would be paid for your time. Sound lovely?

Married couples were welcome. Singles were invited, too. There was even the prospect of romance, provided that those interested in courting remain at least thirty feet apart at all times. It wasn’t that the organisers were prudish, they just cared deeply about sneeze range.

Therein lay the catch, after all there’s no such thing as a free lunch, and certainly not ten free lunches in a row. Every holiday maker had a one in three chance of catching a respiratory infection. The organisers would make sure of it. And still people came by the thousands. Their vacation, they were told, would help cure the common cold.

By the end of World War II, while a number of advances were being made in other human viruses such as influenza and polio, still very little was known about the cold. There was strong evidence that it was viral, but that was it.

Rhinoviruses are so pervasive because their viral surfaces vary widely. The proteins that decorate the outside of the viral shell are inconsistent enough that the antibodies your immune system makes to identify and destroy one serotype simply won’t recognise the next one. Immunologists call this a lack of cross-protective immunity.

In addition to evading immune memory, the different surface proteins can tell us something about the history of the virus. Recently a group of scientists in Japan looked at the differences between the surface proteins on the C group of rhinoviruses, and used them to measure how much time has passed as the virus evolved. The strains they analysed could be dated back to between 400 and 900 years. For example, take the case of the surface protein called VP2. When they looked across all the different rhinovirus serotypes in this group, there was quite a lot of diversity in the gene that makes this protein. They discovered that all the different versions of this gene had a common ancestor sometime around the year 1125. So sometimes your sneezes can be a little bit medieval.

For most people, rhinoviruses are a nuisance, but for some the common cold can have serious consequences. Rhinoviruses can cause acute exacerbations of conditions such as asthma, cystic fibrosis and COPD (chronic obstructive pulmonary disease), so there’s a very real need for a vaccine. Moreover, the economic cost of the common cold has been estimated at an eye-watering $40 billion a year in the US alone in terms of lost work and medical expenses. Even back in World War II, the the common cold had become notorious for its negative impact on the war effort, prompting wary governments to fund post-war programs such as the Common Cold Unit.

Next year will mark 70 years since the first volunteers arrived in Salisbury for their viral holiday, so whatever happened to the common cold vaccine? As it turns out, all those different serotypes weren’t the only problem. Moreover, they might not be as big a barrier as once thought.

Much of the time in the 40s and 50s was spent identifying cold viruses, so it wasn’t until the 60s that vaccine development began in earnest. Researchers were concerned about the increasing number of serotypes, but they had to start somewhere, so early clinical trials began by using a killed version of just one serotype of rhinovirus. The result was underwhelming. They then tried multiple different serotypes at once; still, not much luck. The vaccines just didn’t trigger much of an immune response at all. It’s now thought that this was due in part to an unfortunate catch-22. The techniques used to kill a rhinovirus (so it could be used without causing an infection) were probably damaging many of the protein signatures on the viral surface, the very ones needed for an immune response. It seems that the approach they used to make the rhinovirus vaccine harmless also made it useless.

Why do human rhinoviruses love humans best of all? It has to do with the cells lining your respiratory tract. In order to infect, a rhinovirus must first latch onto a protein called ICAM-1 that sits on the surface of those cells. Mice have ICAM-1, too, but there are enough small differences that human rhinoviruses tend to ignore them. It’s like trying to unlock a different house with the same key. Of course, ICAM-1 was never meant to be a viral access point, even in humans. It’s actually there to help the respiratory tract cells interact with the immune system. But evolution being evolution, human rhinoviruses found a way to use ICAM-1 to their advantage.

A number of researchers are now investigating ways to target ICAM-1 directly and block this viral entry, but it’s a fine line to walk. You want to prevent rhinovirus from latching on yet still allow those normal interactions with the immune system to take place. If you covered your door locks with steel plates, thieves wouldn’t be able to pick the locks, but then you couldn’t use them either.

Curiously, the cotton rat is not new to the study of human viruses. It’s known to be susceptible to a variety of them, including influenza, respiratory syncytial virus (RSV), measles and even polio. But no one knew they also caught our colds.

Then in 2014, another advance was made. It has to do with the fact that rhinoviruses, like all RNA viruses, travel light. They bring little in the way of biological luggage, opting instead to carry a small amount of genetic material. The virus invades the cell and then commandeers the cell’s normal mechanisms to help it make new viruses. As part of this process, the genetic material (RNA) of the rhinovirus provides the instructions to make all the structural proteins it needs to make the viral shell. Instead of these proteins being made one at a time, in the interest of efficiency, one giant protein is made which is then snipped up into individual proteins. This happens in every single serotype.

When a team of researchers in the UK and France examined how these proteins line up back to back in that big precursor protein, they noticed something interesting. Short regions of this big protein are highly similar in almost all of the viruses they examined. Importantly, some of these highly conserved regions are exposed on the viral surface, which means they should be visible to immune cells. One of them included not just VP4, but part of another protein as well — this gave the researchers more to work with than just VP4 alone. It suggested that maybe, just maybe, this snippet of that big protein might work as a vaccine against a wide range of rhinoviruses. So they tried it. They took this region of the protein from one serotype and tested whether it would protect against a different serotype.

It did.

The immunized mice did not get sick, they had no signs of illness at all. There was a clear immune response taking place. The immunized mice produced antibodies to the rhinovirus infection much faster than normal, and they also cleared the virus from their system more rapidly. In vaccinated mice, there was no longer any trace of rhinovirus 4 days after infection. In unvaccinated mice, the virus was still hanging around after 6 days. The findings were published in Plos Pathogens in September, 2014.

So far only a handful of serotypes have been tested and more work is needed to determine whether there is hope of developing a vaccine effective against the many other serotypes in circulation. Nevertheless, it’s a promising proof of concept.

Then, in 1990, the Common Cold Unit closed. They had never found a cure, and a broadly protective vaccine seemed impossible. But it’s now clear that the story is far from over, and we can safely say that they laid the important groundwork for the progress being made today… and that’s nothing to sneeze at.

Today, half the world’s population consumes rice. It’s cultivated in at least 100 countries on every continent except Antarctica. It’s an important staple but also one that’s incredibly sensitive to the vagaries of weather. Both hot and cold cause crop damage, leading to food shortages and financial losses that significantly impact local and national economies.

Of course, this isn’t a new problem. Humans have been consuming rice for millennia. It began with the collection of wild rice species, and then sometime around 8,200 to 13,500 years ago domestication began in what would later become China. Thousands of cycles of selection and breeding have now resulted in two major groups of Asian rice each representing a both a critical trait and a trade-off. Indica rice (O. sativa ssp. indica) is high yield but cold-sensitive. Japonica rice (O. sativa ssp. japonica) has more moderate yields, but is cold tolerant.

The ideal average temperature for growing indica is somewhere around 25 °C / 77 °F, but a mercury dip to 15 °C / 59 °F can wreak havoc if it comes at the wrong time in a plant’s life cycle. This could just be an early frost, a later than usual thaw, or a very cool summer. Japonica, while also a summer crop, can nevertheless handle an average temperature a few degrees Celsius (several degrees Fahrenheit) lower than indica. That may not seem like much, but it means that the minimum temperature is low enough for it to handle unseasonably cool weather as well as farming at higher latitudes or altitudes. It becomes the difference between a good harvest and a failed one.

Both traits in one crop would be ideal, and efforts to produce hybrids have been underway for quite some time, with varying results. But one of the hurdles is the fact that no one really knew precisely why japonica could handle the cold so much better than indica. There was mounting evidence that a variety of different genes are turned on and off in response to cold, but what controls this in japonica was unknown.

In the thousands of years of honing this type of rice for northern climes and higher elevations, it’s reasonable to assume a vast number of genetic differences must have accumulated to result in cold tolerance. However, a team of geneticists in China have now identified a single mutation in just one gene. Their results were published this month in the journal Cell.

They dubbed the gene COLD1, which stands for CHILLING TOLERANCE DIVERGENCE 1 (in the fine scientific tradition of working the name around a good acronym). This gene instructs the cell to make the COLD1 protein. Yun Ma, Kang Chong and their colleagues were able to identify well known patterns in this protein that suggest that it does not float freely within the cell, but is instead embedded in a membrane. If you imagine the membrane as a cloth, and the protein as a thread, then it’s as though it’s been stitched in and out several times in a closely packed pattern. Consequently some parts of the protein sit on the top side of the membrane and some parts sit on the underside.

So how could a slight change in COLD1 help an entire plant become tolerant of cooler temperatures? To find out, the research team first needed to figure out what role the protein normally plays. They identified a series of distinct signatures in COLD1 suggest it belongs to a family of proteins capable of conducting positively charged calcium ions (Ca2+) from one side of a membrane to the other, like a tiny voltage gate.

In indica rice, cooler temperatures decrease the ability of COLD1 to transport calcium ions across the membrane. The influx of calcium slows to a trickle. This in turn has a dampening effect on anything reliant on calcium signals, including pathways that control plant growth and height. Thus, when indica experiences a cold snap, things shut down and don’t recover. It is, in effect, an in-built temperature sensor.

To understand why this happens, we just need to take a quick look at how all proteins respond to changes in temperature. Protein structures have closely packed architectures, and their functions are intricately tuned to disturbances in those structures. At very low temperatures proteins become rigid, at high temperatures, they become less constrained. As such, a protein suited to moderate temperatures becomes too stiff to function in the cold and too floppy to function in the heat. But evolution has been onto this for a while now, give or take a few billion years. This is why proteins in cold loving organisms have looser structures to begin with, so when they tighten up in cold temperatures, they still work. Conversely, proteins in heat loving organisms, such as those found in hot springs, have very rigid structures that loosen up nicely as the temperature rises. It’s also worth noting that that temperature can alter the fluidity of membranes. So if a protein happens to be embedded in a membrane, this can affect its freedom of movement, which in turn can dictate how well it works. Importantly, you don’t have to change a protein’s entire sequence to change its ability to function in a different temperature range or affect the way it interacts with its immediate surroundings. It just has to be the right changes in the right part of the structure and the follow-on effect can be substantial. In japonica it is: when the temperature drops, COLD1 keeps working.

When the researchers compared the genetic sequences of cold sensitive indica rice with cold-tolerant japonica rice they found a change at a single nucleotide, which in turn changes the protein in one place. In indica rice, there is usually a moderately sized, uncharged amino acid at position 187 in the protein sequence (either methionine or a threonine). But in japonica COLD1, amino acid 187 is a lysine — it’s one of the biggest amino acids, and also carries a positive charge.

Somehow that lysine keeps the calcium flowing in cooler weather. It may be that such a disruptive replacement prevents that region of the protein from becoming too rigid, enabling it to maintain its connections with its molecular teammates at lower temperatures. Fluctuations in calcium levels remain possible as the temperature drops, and these in turn are able to trigger important growth signals within the cell.

Ma, Chong and their colleagues also determined that this important genetic change wasn’t a spontaneous mutation that turned up over the last few millennia. Precisely the same mutation exists in the ancient wild rice species called Oryza rufipogon, and this suggests that the farmers who cultivated japonica had deliberately selected this trait as they bred rice to grow in cooler climates. Now we know just what it was they were selecting.

The identification of COLD1 and the variations that affect its behaviour improve our understanding of temperature sensitivity in rice and this knowledge has the potential to significantly impact future breeding efforts. For plant biologists Prabha Manishankar and Jorg Kudla, who reviewed the paper, the implications are far reaching.

“This work may pave the way to tackle the food production insufficiency due to environmental changes and may contribute to food security by stabilizing the yield of a major crop that nurtures a large human population on this planet.”

Deep Look is a wonderful new science video series from KQED. Here they show us how the blue Morpho butterfly actually does not contain any blue pigment. The blue effect is due to the way light scatters off microscopic structures on the wings. Something very similar happens in blue eyes, which also contain no blue pigment at all. Paul Van Slembrouk’s story ‘Structural Eye Color Is Amazing’ on Medium provides a great explanation of why each eye colour looks the way it does.

Thanks to thesciencestudio.org, where I found this gem, and where many more interesting things await.

A little while ago, I wrote an article for Cosmos Magazine on the weird and wonderful history of the earliest known purple pigment. The story begins ancient China, makes a stop in ancient Egypt, finds its way into modern superconductors and winds up in the hands of quantum physicists. There’s also a little bit of Taoism along the way. It’s a strange tale indeed, and still one of my favourites. I hope you enjoy!

late learners benefit, too

Speaking a second language has many obvious practical advantages when it comes to communicating with the wider world. But the question of whether bilingualism confers consistent cognitive benefits, such as better memory or better problem-solving skills, is a topic of much discussion and debate in the fields of psychology and neuroscience. Some studies show distinct advantages, others not so much. But when we look at the effects of bilingualism on the structure of the brain itself, something is definitely going on. Moreover, learning a second language seems to help protect the brain as it ages.

In particular, studies involving people who learned a second language at a very young age show that long term bilingualism has an observable effect on the white matter in their brains. White matter plays an important role in transmitting signals between regions of the brain and within the central nervous system. Some researchers believe that structural changes in the white matter brought on by bilingualism may yield cognitive benefits by improving the connectivity between areas of the brain. There is also evidence that bilingualism helps to preserve the integrity of white matter in old age, and helps protect against cognitive decline. For example, bilingualism appears to delay the onset of Alzheimer’s disease by up to 5 years.

But is this limited to people who began speaking two or more languages at a very young age? In other words, is early-life neurological development an essential part of the picture?

Researchers at the University of Kent and the University of Reading have now shown that late learners can also glean similar benefits from bilingualism. And while the ‘late learners’ in this study began learning a second language relatively young (around 10 years old), it does demonstrate that the structural changes brought on by a second language can happen long after the early stage development of the brain.

There is a catch, though. It seems these changes to the brain, particularly the protection against age-related deterioration, are most likely due to a ‘continuous juggling’ of two (or more) languages. It’s this constant stimulation that helps to preserve the integrity of the white matter. So don’t just take that language course, you need to keep using the language regularly. And yes, this is an excellent reason for that immersion holiday in Provence. You’re welcome. De rien.

the curious tale of the scribbles left behind

Start a blog, I told myself. Then you can write about anything you want.

The idea was enticing, but the promise of writing about anything led very quickly to indecision and that led rather rapidly to no writing at all.

Galaxies, immune cells, archaeological digs, neurons, human behaviour, string theory. Where to begin? Specialise, they say, and there is indeed wisdom in that. But part of the fun of this blog is the chance to explore, to tread new ground, to learn new things, to be amazed, puzzled, delighted, and to then share all of that.

Indecision settled in and grew comfy. I became concerned. Was it really paralysing wonderment? Or was I just chicken? It’s hard to tell some days, but I suspect it’s a bit of both.

I went for a walk to figure it out and on my way I saw a tree. I slowed. I stopped. I took a good look at this tree I’d passed many times before without so much as a glance. Standing there, it became quite clear that if you want to explore the entire universe, you can start quite close to home. This tree had a story. It was, quite literally, scribbled all over it. The markings were rough beneath my fingertips, the author nowhere to be seen.

So this is how the Luminous blog begins: with the story of a tree that took me more than 180 million years into the past.

Let me explain.

The eucalypts grow everywhere around here. This is Australia after all. This neighbourhood was carved out of bushland, and farmland that had once been bushland. But the creeks and the catchments were mostly left alone. There’s a path that winds through. It’s a little bit wild in there, a bit dangerous. It’s marshy in some places, dry in others. Trees tower, some leaning precariously, ready to fall. The underbrush is dense and beautiful. Venomous snakes hide in the tall grass and bulbous spiders dangle patiently on expansive webs.

Some of the wildlife are more benign. There are rainbow lorikeets, kookaburras, and brush turkeys. Recently, I spied a wallaby. It regarded me for a moment then hopped away, almost dismissively. It’s summer now, and the cicadas are singing. They chorus in perfectly synchronised waves, the crests of which are deafening. It thrums in your chest and drowns out the human world. The cicadas are here because they rather like the eucalyptus trees. And the eucalypts, in turn, have brought something else: tiny, elusive writers.

Australia is home to several hundred species of eucalypt. And it seems a modest variety make their home in this narrow stretch of wilderness. One of the most curious is the Scribbly Gum.

The name Scribbly Gum actually refers to a cluster of different eucalypt species found on the eastern seaboard of Australia. Their common signature, as it were, are the scribbles all over their pale, smooth-barked trunks.

These markings have become something of a national icon, weaving their way into Australian folklore and literature.

Australian poet Judith Wright once wrote

The gum-tree stands by the springI peeled its splitting barkAnd found the written trackOf a life I could not read.

The tiny writers are exquisitely shy, they leave their marks and vanish. They’re the elusive graffiti artists of the natural world. The work of beetles, was a common guess. Then, in 1934 the culprit was identified: a moth, scarcely a few millimetres big. A specimen was sent to England into the care of a school teacher named Edward Meyrick. Meyrick, himself, was a curious entity. An amateur entomologist, he had a remarkable hobby of describing, naming, and cataloguing insect species. Moths were a particular favourite. Over his lifetime, he bestowed carefully thought out scientific names to more than 14,000 of them. And so, with due care, he named this one Ogmograptis Scribula. Literally, the writer of the Ogam script. It’s said that he chose the name because the scribbles bore some resemblance to an ancient Celtic writing form called Ogam. There is also a second layer of meaning. Ogmos is not Celtic, it’s Greek; it means furrow – a groove or a narrow trench. When you look closely at the meandering lines on the scribbly gum, you’ll see that’s exactly what they are. For Meyrick, these strange patterns were unique. For all his expertise, his meticulous cataloguing of thousands of moth species, and his passion for taxonomy, Ogmograptis presented an enigma. Where it fit with all the other families, genera and species of moths, he couldn’t say.

And so the story of the diminutive creature remained unreadable for many years. This was exacerbated by the fact that they are difficult to capture in the wild. In defiance of the wide reputation of many moths, Ogmograptis is not lured by light. The larvae are equally recalcitrant. They are so dependent on the eucalypt, they’re difficult to rear in captivity.

In the 1990s, CSIRO entomologist Ted Edwards suggested that the scribbles are formed by the larvae as they mine their way through the bark, feeding as they grow, zigzagging, then doubling back. Still, it was thought there was only one species responsible. Moreover, the scribbles had never been quantified in detail. The math of these moths remained a secret.

photo credit: Natalie Barnett courtesy CSIRO

Then a unique collaboration set the little moth’s story on a new course. Julia Cooke was high school student who wanted to do a project on scribbly gum moths. Edwards had retired, but agreed to mentor Julia. So together they embarked on a study of the scribbles of three different species of eucalypt in the Canberra area. They measured everything they could. The height, the width, the length. The thickness of the furrow, the direction, the distribution. Were they on the north side of the tree, or the south? The east or the west? Were the paths random, or was there something more to it, an innate algorithm? How many zigs, how many zags?

No matter where the scribbles were found, they each showed three clear stages. ‘A’ is the beginning, a very thin random scrawl that follows no rhyme or reason on any tree. ‘B’ is the thicker darker, zigzag, the tunnelling in earnest. ‘C’ is the loop – they all do indeed make a U-turn and follow the path back to the start of ‘B’. And yet, there were distinct differences. For each of the three species of eucalypt they studied, there were slight variations, particularly in the length of the furrow and, remarkably, in the number of direction changes. It was as if these scribbles represented different dialects. A new theory emerged. There wasn’t one species of scribbling moth, there were at least three, possibly more.

Their analysis, particularly the high resolution images of the jaw, linked Ogmograptis with the Australian Tritymba moths and the African Leucoedemia moths. Together they form the southern group of a larger family called Bucculactricidae. The implication of the African connection is profound — it suggests they share a common ancestor who lived on the supercontinent of Gondwana, which comprised the land masses that eventually became the southern hemisphere continents of Australia, Africa, South America and Antarctica (Gondwana also included what is now the Indian subcontinent and the Arabian Peninsula). Indeed, Ogmograptis’ ancestor would have had a home; the recent discovery of a eucalyptus fossil in South America, contributes to strong evidence that eucalypts also have a Gondwanan origin. They seem to have thrived there, and where the eucalypts went the moths followed.

It’s a hot day and I’m walking along the path with my young daughter. Over the song of the cicadas, I tell her to keep an eye out. Smooth bark, not rough, I say. Look for the scribbles.

I see the tree first, but let her find it on her own. “There!” she calls out.

The tree is tall and covered in Ogmograptis graffiti. I cannot tell how far up they go, they disappear into the brightness of the day. There must be thousands of them. We take a good look at the ones right in front of us. My daughter reaches out, picks a scribble that she has decided is the best, traces its path. It follows the pattern perfectly. The random thin scrawl, like a languorous, drunken scratch. Then the regular zigzags, where the larvae grow larger, gnawing through the cork layer. This is why it doubles back. It doesn’t just tunnel, it harvests. It’s a neat trick: the first pass wounds the tree; as the tree repairs itself, it produces a scar tissue – tiny, thin-walled cells full of nutrients. The larvae then does its best 180 — some species have a tighter turning circle than others — and eats its way back again. When it’s had its fill, it bores to the surface, finds its way to the base of the tree, pupates, emerges, and flies away. When the bark sheds, the scribbles are revealed.

photo credit: Fiona McMillan

Somewhere around 180 million years ago, during the Jurassic period, the Gondwanan supercontinent split up. During this slow, tectonic tantrum Australia separated from Africa. Primates had not yet evolved. Dinosaurs roamed, and the world was still millions of years from the asteroid impact that would trigger their demise (well, not all of them, but that’s another story).

Ogmograptis’ life cycle is annual, an evolutionary refinement in keeping with the yearly shedding of eucalyptus bark. The scribbles you see are this year’s scribbles. It is feasible, then, that the scribble my daughter has traced is at least the 180 millionth generation. Arguably more.

It’s time to head back, the day is getting on and my fellow explorer wants lunch. We leave without finding the adult moth, though I didn’t expect to given its reputation for being furtive and so profoundly small. Its body is only 2mm long. It’s wingspan 10-12mm, if that. And yet what it has written, and left behind, is larger than it will ever be itself.

E D Edwards and Marianne Horak “The Scribbly Gum Moth study, Ogmograptis (Lepidoptera: Bucculatricidae)” September 2012 issue of ANICdotes (the official newsletter of the Australian National Insect Collection)